Mean annual temperature trends in the tropical Andes were determined over the last six decades (1939–1998), to investigate the apparent inconsistency between the observed glacier retreat and the reported slight cooling trend in the lower tropical troposphere after 1979. Our results indicate that temperature in the tropical Andes has increased by 0.10°–0.11°C/decade since 1939. The rate of warming has more than tripled over the last 25 years (0.32°–0.34°C/decade) and the last two years of the series, associated with the 1997/98 El Niño, were the warmest of the last six decades. Temperature trends vary with altitude and show a generally reduced warming with increasing elevation. However, despite the lower rate of warming, the trend toward increased temperatures is still significant at the 95% confidence level, even at the highest elevations. Clearly high elevation surface stations in the Andes do not reflect the slight cooling trend observed in the tropical lower‐troposphere.