Monitoring of isotope distribution in the atmosphere included isotopes 2H, 3H and 18O in precipitation, and 13C and 14C in atmospheric CO2. This paper presents the results of atmospheric monitoring over Croatia and Slovenia overt the last few years. Monthly precipitations in Zagreb and Ljubljana had been collected since 1976 and 1981, respectively. Between 2000 and 2003 monitoring also included seven stations along the Adriatic coast. Tritium activity in precipitation shows seasonal variations that were most pronounced inland (at the continental stations Zagreb and Ljubljana) and were the smallest in the south Adriatic (Komiza and Dubrovnik). Mean annual tritium activity decreases from the north to the south Adriatic coast. Seasonal variations in delta2H and delta18O in precipitation follow the temperature variations at the sampling stations. Atmospheric CO2 was collected in Zagreb and Plitvice as a composite monthly sample. Both delta14C and delta13C showed seasonal variations. The mean annual 14C activities in Zagreb had been decreasing after the peak reached in the 1960s, and for the last three years the mean 14C activity (delta14C) remained about 30 per thousand.