It is generally accepted that the severity of renal insufficiency in patients correlates with the severity of tubulointerstitial abnormalities, but not with the severity of glomerular abnormalities in kidney biopsies. We recently challenged this view by demonstrating significant correlations of glomerular structural abnormalities with renal function in a histomorphometric study of biopsies from patients with various kidney diseases. We set out to confirm these findings in biopsies from patients with a single disease entity. IgA nephropathy was selected. An additional objective of the study was to determine the prognostic value of our histological predictors of renal function. Histomorphometric measurements were done in silver- and PAS-stained paraffin sections of biopsies from 83 patients with primary IgA nephropathy. The results were correlated with creatinine clearance at the time of biopsy. The prognostic value of the histomorphometric parameters and of several clinical characteristics were determined in a Cox proportional hazard model. All glomerular histomorphometric indices correlated with the severity of renal insufficiency, but quantitative estimates of the glomerular deposition of periodic acid-Schiff positive extracellular matrix (PAS-index) seemed to be the most important glomerular structural-functional correlate (r = 0.53, p<0.001). However, the correlation of quantitative estimates of the severity of interstitial extracellular matrix accumulation with renal function (quantitative interstitial index) was superior (r = 0.76, p<0.001). Creatinine clearance at biopsy and initial proteinuria were the strongest clinical predictors of renal survival. The severity of tubulointerstitial extracellular matrix accumulation was the strongest histological predictor of an adverse outcome. In conclusion, quantitative estimates of the severity of glomerular and tubulointerstitial extracellular matrix accumulation both correlate well with the severity of renal failure in biopsies from patients with IgA nephropathy. Creatinine clearance at biopsy, initial proteinuria and the severity of tubulointerstitial extracellular matrix accumulation are the best predictors of renal survival. On a more general note, the paradigm of the absence of correlation of glomerular pathology with renal function should be abandoned.