Recent studies on avian parentage have used both biochemical techniques and field observations to detect intraspecific brood parasitism and extra-pair fertilizations (EPFs). In long-term parentage studies of the European Starling (Sturnus vulgaris) using electrophoresis and field observations, we have encountered several methodological problems. Based on our findings and the existing literature, we describe these pitfalls and suggest improvements in techniques. The pitfalls include difficulty in obtaining large sample sizes, manipulation of natural populations, inaccurate allelic frequencies based on electrophoretic screening of too few individuals, catching the wrong putative parents, improper storage and handling of tissue samples, confounding effects of developmental changes in allelic expression, and misinterpretation of electrophoretic results. To improve parentage studies, we suggest censusing nest boxes around the peak times of laying to detect more than one egg per day, matching nestlings with eggs, establishing strict criteria for identifying putative parents at a nest, collecting pectoral muscle using an incision that goes in the direction of the superficial pectoral muscle fibers, and assessing the relative efficiency of laboratory and field methods to decide which would yield maximum results.