This study had the aim of analyzing the spatial and temporal distribution of autochthonous malaria cases according to parasite density, symptoms and activity at the time of infection. A retrospective descriptive study was undertaken in the municipalities of Ubatuba, Caraguatatuba, São Sebastião and Ilhabela, covering 1985 to 2006. The data were obtained from the epidemiological investigation files of the Superintendency of Endemic Disease Control and the Information System for Health Threat Notification. Out of the 83 cases notified, 77% were male. São Sebastião and Caraguatatuba presented the largest numbers of cases. The individuals most affected with Plasmodium vivax were at productive ages, with a parasite density of one parasite for every two or more microscope fields. At the time of becoming infected, these patients were mostly doing leisure activities. The main symptoms were fever, headache, sweating and myalgia. Four asymptomatic cases were detected. These data are expected to contribute towards improving the decentralized malaria control actions in the region, through considering malaria among the clinical and/or epidemiological suspicions, with a reference laboratory and trained personnel for adequate diagnosis and treatment.