The levels of polychlorinated dibenzo-p-dioxin (PCDD) and polychlorinated dibenzofuran (PCDF) or polychlorinated biphenyl (PCB) in foodstuffs have decreased over the past decade in many countries. However, the trend for the levels of these compounds in foodstuffs in Taiwan remains unknown. In this study, we compared the distribution of PCDD/F and PCB in nine foodstuff categories acquired from Taiwan markets from 2004 to 2012. The levels expressed as World Health Organization toxic equivalents (WHO-TEQs) in the different foodstuffs tested were as follows: fish, average 0.463 pg WHO-TEQ/g sample > seafood, 0.163 pg WHO-TEQ/g > eggs, 0.150 pg WHO-TEQ/g > oils, 0.126 pg WHO-TEQ/g > meats, 0.095 pg WHO-TEQ/g > dairy products, 0.054 pg WHO-TEQ/g > cereals, 0.017 pg WHO-TEQ/g > vegetables, 0.013 pg WHO-TEQ/g > fruits, 0.009 pg WHO-TEQ/g. Levels were particularly high in crab (average: 0.6 pg WHO-TEQ/g sample (1.243 pg WHO-TEQ/g sample) and large marine fish (0.6). In Taiwan, a decreasing trend of PCDD/Fs or dioxin-like PCBs (dl-PCBs) was observed in meat, dairy, eggs, and vegetables, whereas an elevated trend was observed in cereals or the levels were nearly equal in fruits and oils at alternative time shift. Dl-PCBs contributed to 60-65% toxicity equivalence levels in fish and seafood, but only to 13-40% in meat and cereal samples. The decreasing trend was consistent with the results in other countries; however, the trends in cereals, fruits, and oils were in contrast to previous results reported in other countries. Cereals and fruits are important crops in southern Taiwan, and the local pollution generated by industries or incinerators may seriously affect the distribution of PCDD/Fs and dl-PCBs. To ensure food safety, a risk assessment for residents living in different areas should be adopted for all food categories simultaneously in the future.