Anthropogenic effects on ecosystems are one of the main causes of reduction in the planet's biodiversity. The present study aimed to assess the effect of habitat disturbance on the body condition of the Colombian endemic lizard Anolis antonii. Two populations from the department of Tolima (Colombia) were chosen for this work, one located in a secondary forest and the other in an agricultural area. Between January–June 2014, visual encounter surveys were simultaneously performed from 7:00–18:00 h in both habitats. Individuals were captured manually and sex, snout-vent length (SVL) and body mass (BM) were recorded for each. The Body Condition Index (BCI) was calculated from the residuals of the linear regression between BM and SVL, which was compared between the two populations (60 adults in the secondary forest and 52 in the agricultural area). No significant variation in SVL or BM was recorded in the inter- and intra-population comparisons, but the BM of lizards was closely related to SVL and the BCI of the population from the agricultural area was significantly lower than that of the secondary forest population. These results indicate that habitat disturbance as a consequence of agricultural practices has a negative impact on the body condition of A. antonii, which could reduce its abilities to compete and survive.