The severity of cutaneous leishmaniasis may be determined by host immunity, parasite virulence, and host or vector behavior. We performed a multivariate analysis to identify the main causes of the variability in clinical symptoms, response to treatment, and parasite isolation rate among Peruvian patients. The effect of host immunity was demonstrated first by the finding that secondary infections induced smaller lesions associated with a lower parasite isolation rate than did primary infections and, second, by the finding of fewer lesions in older patients. Phenotypic differences between parasite populations were suggested by the observation that the mean scar size and number varied between villages: patients had more scars in villages where the transmission rates were higher. Human behavior probably determined the site of lesions on the body, since most lesions in the cooler South were on the head, whereas in the North, lesions were equally frequent on the extremities. In addition, older patients, who were more likely infected through occupational exposure, had fewer head lesions. Geographic variation in the pattern of exposure to sandflies indicates that uta control strategies should be region specific.