AbstractPhytosterols are natural compounds that contribute to lower serum cholesterol in humans. Sunflower seeds and oils are rich sources of phytosterols. Breeding for phytosterol content in sunflower has been scarce thus far, mainly because of the lack of analytical methods suitable for use in plant breeding. The objective of this research was to validate a method for the analysis of phytosterols in small seed samples of sunflower. Samples consisting of six seeds were analyzed for phytosterol content in a set of 87 inbred lines using a method adapted to small samples. The accuracy of the method was evaluated through the standard error of the analysis of replicates of ground samples, which was 72.12 mg/kg compared to average values of 1665.3 and 1887.2 mg/kg seed in the samples. Sunflower inbred lines showed ranges of variation from 1426.0 to 4710.0 mg/kg seed and from 2855.2 to 9752.0 mg/kg oil. The method correlated strongly with the conventional method based on the analysis of extracted oils (r = 0.85). The results indicated that analysis of phytosterols on samples consisting of sunflower seeds is an accurate approach for breeding and genetic studies, in which extraction of the seed oil is not feasible.Practical applications: Phytosterols are usually analyzed in extracted oils. However, studies in plant breeding and plant sciences often require a direct analysis of phytosterols in seeds, without previous oil extraction (e.g. large‐scale screening of germplasm in breeding programs or genetic studies). Our results will be useful for plant scientists interested in the analysis of phytosterols in small samples of plant tissues.