This study assessed the state of health economic evaluation (including pharmacoeconomic) research in Nigeria. A literature search was conducted to identify health economic articles pertaining to Nigeria. Two reviewers independently scored each article in the final sample using a data collection form designed for the study. A total of 44 studies investigating a wide variety of diseases were included in the review. These articles were published in 34 different journals, mostly based outside of Nigeria, between 1988 and 2009. On average, each article was written by four authors. Most first authors had medical/clinical affiliations and resided in Nigeria at the time of publication of the study. Based on a 1 to 10 scale, with 10 indicating the highest quality, the mean quality score for all studies was 7.29 (SD 1.21) and 59% of the articles were of fair quality (score 5-7); 5% were of even lower quality. The quality of articles was statistically significantly (p < or = 0.05) related to the country of residence of the primary author (non-Nigeria = higher), country of the journal (non-Nigeria = higher), primary objective of the study (economic analysis = higher) and type of economic analysis conducted (economic evaluations higher than cost studies). The conduct of health economic (including pharmacoeconomic) research in Nigeria was limited and about two-thirds of published articles were of sub-optimal quality. More and better quality health economic research in Nigeria is warranted.