The tropical, warm, and humid conditions that are favorable to the growth and development of mycotoxigenic fungi put the Philippines at a high risk of mycotoxin contamination. To date, seven mycotoxigenic Aspergillus species, four Fusarium species, and one Penicillium species have been isolated from various agricultural crop commodities in the country. There are five mycotoxin groups (aflatoxin, fumonisin, ochratoxin, nivalenol, and zearalenone) that have been detected in both the raw form and the by-products of major crops grown in the country. Since the first scientific report of aflatoxin contamination in the Philippines in 1972, new information has been generated on mycotoxins and mycotoxigenic fungi, but little has been known of other mycotoxins until the last two decades. Further, despite the increase in the understanding of mycotoxigenic fungi and mycotoxins in the country, very limited knowledge exists on practices and measures that control both the fungi and the toxins. This paper reviews the current literature on mycotoxigenic fungi and mycotoxins in the Philippines with emphasis on the last two decades and on other mycotoxins.