Vegetables are considered as an important part of a healthy diet. However, there have been reports showing contamination of vegetables with parasites. This study aimed to assess parasite contamination of freshly harvested vegetables from selected organic and conventional farms in the Philippines. A total of 252 freshly harvested vegetables were collected from 20 farms through systematic random sampling and were processed by means of sedimentation technique. Positive samples were subjected to molecular analysis for further identification of species. Results showed that 58 out of 252 (23.02%) vegetable samples were contaminated with parasites eggs/cysts/oocysts. The parasites found were Ancylostoma ceylanicum, Toxocara sp., Trichuris trichiura, Ascaris suum, Hymenolepis sp., unknown trematode egg, Isospora, Balantidium, Giardia intestinalis and Cryptosporidium. Ascaris suum had the highest contamination rate in organic and conventional farms at 13.09% and 8.33%, respectively. Cryptosporidium (≥800 oocysts/ kg) and Giardia intestinalis (≥240 cysts/kg) had the highest mean density in both farms. Also, lettuce showed the highest contamination rate among the sampled vegetables in both types of farms. Furthermore, results revealed that texture of vegetables, distance to the soil substrate, and farming practices could possibly contribute to the parasite contamination of vegetables in this study. These findings have important implications on public health that may aid regulatory agencies for prevention and control strategies for food safety.