Hand, Foot and Mouth Disease (HFMD) is an emerging viral disease, and at present, there are no antiviral drugs or vaccines available to control it. Outbreaks have persisted for the past 10 years, particularly in northern Thailand. This study aimed to elucidate the phenomenon of HFMD outbreaks from 2003 to 2012 using general statistics and spatial-temporal analysis employing a GIS-based method. The spatial analysis examined data at the village level to create a map representing the distribution pattern, mean center, standard deviation ellipse and hotspots for each outbreak. A temporal analysis was used to analyze the correlation between monthly case data and meteorological factors. The results indicate that the disease can occur at any time of the year, but appears to peak in the rainy and cold seasons. The distribution of outbreaks exhibited a clustered pattern. Most mean centers and standard deviation ellipses occurred in similar areas. The linear directional mean values of the outbreaks were oriented toward the south. When separated by season, it was found that there was a significant correlation with the direction of the southwest monsoon at the same time. An autocorrelation analysis revealed that hotspots tended to increase even when patient cases subsided. In particular, a new hotspot was found in the recent year in Mae Hong Son province.