Inorganic rockwool breaks down slowly after it was used which makes it a environmental problem. Research was done in 2015, with the objective to investigate the influence of local organic and mixed substrates on the yield components of pepper and to compare it with the results obtained on rockwool. Research was conducted in a greenhouse on the experimental field of the Department of Vegetable Crops, Faculty of Agriculture in Zagreb. Three pepper cultivars were tested (Irene, Cara, Kalifornijsko čudo) and were planted on rockwool and organic and mixed substrates (organic with slow release fertilizer). The experiment was set up according to the complete randomized block design with four replications. Planting was done at a distance of 120 cm between rows and 33 cm within the rows which represents a set of 2.5 plants per m2. Minimum and maximum air temperatures and relative humidity were measured daily during the vegetation. Greenhouse peppers were pruned on two stems in a V-cordon form. Five harvests were done from July 1st to August 14th. Number and weight of marketable fruits was determined along with marketable yield and the share of non-marketable fruits with blossom end-rot symptoms in the total number of fruits. Statistic analysis of the results was done by variance analyze (ANOVA) while the differences between average values were determined using LSD test. All tested cultivars developed marketable fruits with satisfactory mass above 100 g. Type of substrate significantly influenced the number and yield of marketable fruits. The cultivars grown on rockwool provided significantly higher number of marketable fruits in relation to the organic substrate or mixed organic substrate, which resulted with higher marketable yield. Type of substrate did not significantly affect the mass of marketable fruits. Significant differences were not observed between cultivars and substrate in the share of non-marketable fruits.