<p><strong>Abstract.</strong> The Asian summer monsoon anticyclone (ASMA) is a major meteorological system of the upper troposphere-lower stratosphere (UTLS) during boreal summer. It is known to be enriched in tropospheric trace gases and aerosols, due to rapid lifting from the boundary layer by deep convection and subsequent horizontal confinement. Given its dynamical structure, the ASMA offers a very efficient pathway for the transport of pollutants to the global stratosphere. Detailed understanding of the ASMA structure and processes requires accurate in-situ measurements. Here we present balloon-borne measurements of temperature, water vapor, ozone and aerosol backscatter conducted within the StratoClim project from two stations at the southern slopes of the Himalayas. In total we performed 63 balloon soundings during two main monsoon-season campaigns, in August 2016 in Nainital, India (NT16AUG) and July&#8211;August 2017 in Dhulikhel, Nepal (DK17), and one brief post-monsoon campaign in Nainital in November 2016 (NT16NOV). These measurements provide unprecedented insights into the ASMA thermal structure and its relations to the vertical distributions of water vapor, ozone and aerosols. To study the structure of the UTLS during the monsoon season, we adopt the thermal definition of tropical tropopause layer (TTL), and define the region of altitudes between the lapse rate minimum (LRM) and the cold-point tropopause (CPT) as the Asian Tropopause Transition Layer (ATTL). Further, based on air mass trajectories, we define the Top of Confinement (TOC) level of ASMA, which divides the lower stratosphere (LS) into a Confined LS (CLS), below the TOC and above the CPT, and a Free LS (FLS), above the TOC. Using these thermodynamically-significant boundaries, our analysis reveals that the composition of the UTLS is affected by deep convection up to altitudes 1.5&#8211;2&#8201;km above the CPT due to the horizontal confinement effect of ASMA. This is shown by enhanced water vapor mixing ratios in the Confined LS compared to background stratospheric values in the Free LS, observed in both NT16AUG (+0.5&#8201;ppmv) and DK17 (+0.75&#8201;ppmv), and by enhanced aerosol backscatter of the Asian tropopause aerosol layer (ATAL) extending into the Confined LS, as observed in NT16AUG. The CPT was 600&#8201;m higher in altitude and 5&#8201;K colder in DK17 compared to NT16AUG and strong ozone depletion was found in the ATTL and CLS in DK17, suggesting stronger convective activity during DK17 compared to NT16AUG. An isolated water vapor maximum in the Confined LS, about 1&#8201;km above the CPT, was also found in DK17, which we argue is due to overshooting convection hydrating the CLS. These evidence show that the vertical distributions and variability of water vapor, ozone and aerosols in the Asian UTLS are controlled by the top height of the anticyclonic confinement in ASMA, rather than by CPT height as in the conventional understanding of TTL, and suggest that the ASMA contributes to moistening the global stratosphere and to increase its aerosol burden.</p>