Abstract Leaf compounds may contribute to plant defense against Cronartium rusts. Secondary compounds are either natural or induced in leaves. We studied the variation of compounds in leaves of six alternate hosts of Cronartium pini and two of C. ribicola that represented either susceptible or resistant species to these rusts. Extracts from the plant leaves were analyzed using LC-MSMS (liquid chromatography tandem mass spectrometry) and compounds were compared between susceptible and resistant species of the same plant genera to identify significant differences between resistant and susceptible species. Also, LC–MS (liquid chromatography mass spectrometry) with external calibration was used to quantify 12 candidate compounds known from the literature. Among these compounds, the most abundant significant ones in C. pini -resistant Melampyrum pratense were chlorogenic acid and quercitrin, in Veronica chamaedrys ferulic acid, quercitrin and luteolin and in Impatiens glandulifera quercitrin, ferulic acid, kaempferol, rutin and hyperoside. In C. ribicola -resistant Ribes rubrum the most abundant significant compounds were caffeic acid, p-coumaric acid and quercitrin. Among all extracted leaf compounds, concentrations of three compounds were over 1000 times greater in rust-resistant M. pratense, three compounds in V. chamaedrys, eight compounds in I. glandulifera, and one compound in R. rubrum than in rust-susceptible species. Among the compounds, the most promising possibly linked to rust resistance were chlorogenic acid and quercitrin.