Milk thistle (Silybum marianum (L.) Gaertn.) is an important medicinal plant. Achenes of milk thistle contain sylimarin, protecting liver cells against toxic compounds. The aim of the research was to find an optimum method of evaluation of milk thistle seed germination. Ten seed samples were tested. The seeds were germinated: on top of blotter paper, on top of blotter paper after seed disinfection, between pleated blotter paper, in rolled blotter paper and in sand. Germination at the first and final counts, the percentages of abnormal seedlings and dead seeds were determined. The correlation coefficients between seed germination, evaluated with various methods, and seedling emergence were calculated. Moreover, fungi associated with seeds and diseased seedlings were identified. The lowest percentage of normal seedlings was observed after germination on the top of blotter. Highly significant positive correlations were noted between seedling emergence and seed germination at the final count evaluated in rolled paper, between pleated paper and in sand. The fungi from genera:Alternaria, Fusarium, Penicillium, Trichoderma, Ulocladium and Verticillium were frequently identified on seeds and seedlings. Infestation with fungi significantly affected milk thistle seed germination and plant emergence. Germination in rolled blotter paper may be recommended for evaluation of milk thistle seed germination, as the most practical and significantly correlated with seedling emergence.