We used electron microscopy (EM) to analyze 52 biopsy samples from 22 patients who were receiving long-term weekly oral doses of methotrexate (MTX) for the treatment of rheumatoid arthritis. Forty-eight biopsy samples were obtained after 2-6 years of continuous treatment, and 4 samples were obtained before treatment was begun. Specimens were graded for neutral fat, secondary and tertiary Iysosomes, and smooth endoplasmic reticulum (SER) in hepatocytes, and for collagen in the perisinusoidal space (Disse's space). We examined the correlations between the EM findings and the light microscopic (LM) findings in the same biopsy specimens, and between the EM findings and the results of simultaneous monthly measures of aspartate transaminase, alkaline phosphatase, bilirubin, and albumin levels, as well as history of alcohol consumption before MTX treatment and monthly assessments of clinical status during the course of treatment. The presence of collagen was minimally increased in these sequential biopsy samples, whereas fat, lysosomes, and SER were decreased. The SER decrease was statistically significant. EM findings of collagen in the space of Disse did not correlate with early fibrotic changes observed with LM. Thus, after as long as 6 years of weekly oral treatment with MTX, hepatic ultrastructural changes are minimal and are not clinically significant. The use of EM for sequential biopsy studies allows the quantitation of long-term hepatic changes that may be more limited than the impression gained after LM analysis.Methotrexate (MTX) is an effective agent in the treatment of refractory rheumatoid arthritis (RA) (1-lo), but there are concerns about its long-term use. The potential for toxic effects involving the pulmonary (11-15) and hepatic (16-19) systems have been documented. Risk factors for the development of hepatotoxicity have been well defined in patients with psoriatic arthritis (16,2&22); these factors include a history of alcohol abuse, obesity, and advanced age at the time of initiation of MTX therapy.We have previously examined multiple variables that assess the progression of hepatic abnormalities in liver biopsy specimens from patients with RA who have been taking MTX, and we have found similar risk factors in this population (23). Although the incidence of cirrhosis in patients receiving MTX for psoriatic arthritis is high (16,(20)(21)(22), the frequency of serious hepatotoxicity occurring in patients receiving the drug for treatment of RA is quite low (16)(17)(18)(19)(23)(24)(25)(26). In an earlier study using light microscopy (LM) to examine liver biopsy samples, however, we observed the beginnings of fibrotic changes in samples from 56% of the RA patients who had taken MTX for a mean period of 53 months (23).To determine whether the changes that are detectable by electron microscopy (EM) are more sensitive indicators of the beginning of hepatic abnormalities in RA patients, we examined sequential liver biopsy specimens (obtained annually during treatment) with both LM and EM. Preliminary result...