In this study we examine the effect of natural perturbations on cirrus cloud cover in the tropics and we look for possible signal of cirrus contrails in tropical air traffic regions focussing on Southeast Asia, a region that has received much less attention than the well investigated North Atlantic and North American air traffic corridors. The analysis is based on the latest version of the ISCCP D2 cirrus cloud dataset and covers the period 1984 - 2000. Four parameters were examined for their relation with cirrus cloud trends: deep convective clouds from ISCCP, vertical velocities, relative humidity and air temperature at 200 mb from ECMWF/ERA40. The results show that there is a strong correlation between cirrus clouds and dynamical parameters (deep convective clouds, vertical velocities) over Southeast Asia, explaining a significant part of the tropical cirrus cloud variability. After removing seasonality, the ENSO signal becomes dominant on cirrus, on deep convective clouds and on vertical velocities over regions of the western and the eastern tropical Pacific Ocean. Over Southeast Asia, the average decrease in cirrus during the strong 1997/98 El Nino event was about 6% cloud cover or ~25% of the regional mean. In order to search for possible signal of cirrus contrails over S. E. Asia, we calculated trends in cirrus coverage over tropical regions with high air traffic after removing the ENSO effect. The results show that there is a small positive trend in cirrus clouds over the S. E. Asia air corridors during winter (+0.1% cover/decade), which is not statistically significant and is related to small positive trends in deep convective clouds. In summer, cirrus clouds are anti-correlated with deep convective clouds over this region and the trends are opposite. The negative trends in cirrus clouds, which are observed in the summer (-4.5% cover/ decade), are related to trends in dynamical and thermo-dynamical parameters. It is shown that cirrus clouds are statistically significant correlated with vertical velocities and air temperature at 200 mb (correlations of -0.7 and -0.6, respectively), explaining the highest part of the long-term variability of cirrus clouds over S. E. Asia. Over the Caribbean air corridors, on the other hand, there are significant increases in cirrus cloudiness by about 2.5% per decade in winter (99% confidence level) and 2.7% cover/ decade in the summer (95% confidence level), part of which is also related to trends in dynamical and thermo-dynamical parameters. According to our findings, it is difficult to detect possible effects of regional persistent contrails on cirrus cloud trends over the S. E. Asia air traffic corridors. This is because in winter there are not statistically significant trends in cirrus clouds and in summer trends in dynamics and thermo-dynamics mask this issue. Taking also into account that flight frequencies and fuel consumption are moderate over the tropical air traffic corridors, it makes it even more difficult to detect and quantify any possible anthropogenic effects.