The paper by Mazzini et al., investigates aerosol number size distributions (PNSD) and new particle formation (NPF) in the free troposphere (FT) using long-term measurements from two high-altitude observatories, Monte Cimone (2165 m, Italy) and Jungfraujoch (3580 m, Switzerland). The aim is to understand how aerosol formation, growth, and variability differ between the two sites. The results show that CMN is affected by more frequent and intense NPF and stronger PBL influence, while JFJ shows fewer NPF events, weaker growth despite more ultrafine particles. This is a good quality study that makes an important contribution to understanding aerosol formation in the free troposphere (FT). It is especially valuable because it contrasts two representative European high-altitude sites, applies three independent NPF classification methods and is based on a solid dataset consisting of two years of harmonized measurements. The paper also highlights how the condensation sink, cloud processes and boundary-layer strongly regulate NPF, providing a strong link between observations and their climate relevance.

The manuscript is well written and carefully developed. With the addition of some clarifications and details, it should be suitable for publication.

Specific comments:

Line 6: Sometimes “free troposphere (FT)” written in full, sometimes only “FT.” Suggest spell out first time and then “FT” for consistency.

Line 29: “The frequency of NPF events vary widely” → should be “varies widely.”

Line 59: “at 2165 m a.s.l..”  double period. Should be “a.s.l.”

Line 63: the sentence  “with this influence being most pronounced during summer daytime hours and diminishing at night, when the site predominantly reflects free tropospheric characteristics” is too long. I Suggest splitting into two sentences.

Line 63: “2.5–560nm” should have space: “2.5–560 nm.” Please check the entire document.

Line 97: Datasets coverage: “31.2% at CMN… In contrast, summer months show notable data gaps”. Could you provide the percentage of the different seasons for clarity?

 Line 102: “originating from the nucleation of gas-phase precursors forming clusters approximately (∼1–2nm)”; parentheses awkward, just write “forming ∼1–2 nm clusters.”

Line 104: “Scaling factors were derived individually for each measured size distribution, and applied to all NAIS channels accordingly.” Please remove comma before “and.”

Line 107: “a common range of 2.5–560nm”  should be “2.5–560 nm” (space before nm). Please check the entire document.

Line 149 and 150: Equation 2 formatting inconsistent: bracket notation N[2.5−7) inconsistent with earlier N2.5−7. Please harmonize notation.

Line 161-163: about RH threshold, you define out-of-cloud as RH < 94%, in-cloud as > 97%. But what about 94–97%? Please clarify explicitly.

Line 163:  “Webcam images were used to further validate cloud presence”,  could specify frequency or reliability (continuous, daily snapshots?).

Line 171: “(770−3)”  should be “(770 cm⁻³)”.

Line 171:  “across four defined mode” should be “modes.”

Line 206: “These categories reflect distinct stages of aerosol…….These modes reflect distinct stages of particle growth and transformation”,  the two repeated sentences are redundant. Please rephrase them

Line 210: In Table 2, confidence intervals are in parentheses but not explained in caption. Please clarify.

Line 227: “These elevated ratios has been observed” should be “have been observed.”

Line 233: “One more possible explanation for the relative abundance…”,  awkward phrasing, better “Another possible explanation…”

Line 243: Figure references: sometimes “Fig. X,” sometimes “Figure X.” Pick one style.

Line 265: “Ions also shows different behaviour between out-of- and in-cloud” should be “Ions also show different behaviour between out-of-cloud and in-cloud conditions”

Line 274:  Table 3 should be harmonized (e.g., JFJ summer values missing ±).

This study by Mazzini et al. compares two years of observations of aerosol size distribution data at two high-altitude GAW stations in central Europe, Jungfraujoch (JFJ) and Monte Cimone (CMN). The focus is on the frequency and strength of New Particle Formation (NPF) and the abundance of ultrafine particles. As free tropospheric aerosol production is important in the climate system, such high-altitude location studies are interesting tool to investigate the processes related to NPF in the free troposphere and its coupling to the planetary boundary layer. The manuscript is well written, uses appropriate methods to analyze NPF and gives some insights into the role of boundary layer influence on free tropospheric processes. It merits publication in Atmos. Chem. Phys.. Apart from some minor points, I have some concerns about the merging of NAIS and SMPS for the combined particle number size distribution (PNSD) which should be addressed carefully, before publication.

Major comments:

• The authors describe a procedure to combine the NAIS particle mode data with the SMPS data to obtain a merged PNSD. In the overlapping size range, they derive scaling factors which are then applied across the entire NAIS dataset. This is problematic, as the NAIS offset to SMPS data might not be constant across all sizes, as its origin is partly due to unknown multiple charged particles in the larger sizes and agreement is often better at smaller sizes (Kangasluoma et al., 2020). This might induce some considerable error on the absolute number concentrations derived for the modes measured mainly with NAIS and the percentage shares in Figure 2 might therefore be highly uncertain. In addition to that the SMPS sample is dried, and the NAIS is not, according to the description. This introduces some additional uncertainty in the merging of the two instruments, as PNSD are merged at the same diameter, while the one might be dry and the other might be a wet diameter. The authors should investigate the overlap of the size distribution in dependence on RH to see if there is a significant difference. Last, I couldn’t find an explanation why different size ranges are used for JFJ and CNM to merge the size distributions. This should be clarified.
  
  The best approach to address all these concerns would be a comparison of the integrated merged PNSD with a CPC measuring the total number concentration of aerosol particles, which to my knowledge should at least be available for JFJ.

Minor comments:

• Line 110: Technically the survival probability (growth versus coagulation loss) is even lower for the intermediate mode and therefore fast growth even matters more there.
• Line 139: Clarify in the text what the variables Max(ΔN3-6)active and Median(ΔN3-6)non-active represent.
• Line 142: The presence of small particles at high RH is attributed to cloud processing and not instrument artefacts here. Is there any reference the authors can provide?
• Line 161: Related to the above: What does it mean the PNSD remained stable? Anything quantitative?
• Line 168: unit missing
• Line 176: The higher fractional share of Aitken mode particles at CMN does not necessarily mean that survival of NPF particles is enhanced (the share could just be higher as the “background”, i.e. accumulation mode, is overall lower at JFJ. In fact, when comparing nucleation mode to Aitken mode concentrations they are more similar at JFJ in terms of absolute numbers, indicating a lower loss.
• Line 179: In the same sense the absolute concentrations of the accumulation mode at CNM are twice as large as at JFJ (while the relative share doesn’t increase that much).
• Line 181: Fig 3 is referenced while the text probably references to Fig. 2 and moreover the total number concentrations across the seasons are never shown.
• Figure 3 deserves a more detailed caption explaining the shaded areas (interquartile ranges) and colors.
• Line 194: There seems to be sometimes a kind of bimodal pattern in the intermediate particles both at JFJ and CMN. Any explanations for this? Showing some median diurnal PNSD (as surface plots) in the Supplement would help to better understand what is shown in Fig. 3.
• Line 198: I am struggling with the word “nucleation efficiency”. What does it mean? High GR, low sink, high J or just high GR and low sink?
• Line 228: I think that “personal communication” is not a valid citation in Copernicus journals.
• Line 229: The lower negative cluster ion concentrations are also very much related to reduced sensitivity of the instruments towards these highly mobile ions. Negative cluster ions have on average higher mobilities than positive cluster ions and more easily get lost in the inlet system. Without perfect corrections for this, their measured concentration will be lower due to higher losses. This should be mentioned here clearly.
• Line 310: Or the lower absolute accumulation mode background at JFJ allows an easier detection of smaller changes, i.e. few grown particles reaching accumulation mode sizes, which would not be detectable at CNM.
• Figure 9: The coloring for the ion plot could have better contrast.
• Line 318: It reads like sulfuric acid stabilizing the early clusters, while in fact, it might be the main component of them. The ions are stabilizing the cluster. Please rephrase.
• Line 331-333: The authors discuss some results here without showing the data or referencing it.
• Line 334: Isn’t the warmer temperature also indicative for a higher PBL air mass intrusion?
• Line 345: The statement that clean atmospheric conditions are needed for enabling nucleation and early particle growth is partly correct, but here and, mor importantly, also in the conclusions I am missing the following thought process: While a lower CS is better, at JFJ we see that if the conditions get too “clean” in a sense of less boundary layer interaction (the real FT) we are at the same time missing the precursor vapors. It seems to be a very delicate balance between having clean conditions in terms of low background and at the same time a high abundance of precursor vapors such that NPF proceeds efficiently. This is seen at many places around the world (in megacities, too high CS typically prevents NPF, still NPF is possible to proceed at higher CS than in rural regions as also more precursors are available). I think the comparison between JFJ and CMN shows exactly this: Cleaner conditions in term of background do help, but we also need the precursors, which at CMN are more abundant. This argument should be brought forward very clearly in a revised discussion.
• Line 358: I guess summer data doesn’t provide enough statistics to really conclude this (no SD given in the Table, so I assume the number relies only on two values).