The intercountry border areas of Thailand have high malaria receptivity and vulnerability that present numerous problems in the control of malaria transmission. This study focused on the 30 provinces of Thailand situated next to neighboring countries, which can be divided into 4 groups: the Thai-Myanmar border (10 provinces), the Thai-Cambodia border (6 provinces), the Thai-Lao border (10 provinces) and the Thai-Malaysia border (4 provinces). The purpose of the present study was to describe the pattern and trend of malaria incidence in the highly endemic provinces along the Thai borders for the 11 years from 1991 to 2001. Analysis of trends showed the distribution of malaria parasites to have shifted from a preponderance of Plasmodium falciparum to Plasmodium vivax along the western border with Myanmar, the northern border with Lao PDR and along the eastern border with Cambodia whereas the southern border with Malaysia the pattern changed from a preponderance of P. vivax to P. falciparum, since 1997. There was a significant difference in annual parasite incidence between borders and non-border districts, especially along the Thai-Myanmar and Thai-Cambodia borders. It is thus evident that all border districts should pay more attention to control of malaria transmission and the activities of the malaria surveillance system, and that monitoring and evaluation of the Thai Malaria Control Program needs to be performed consistently, including some areas where a few malaria cases were found as well as in malaria free areas.