Cucumber (Cucumis sativus L.) is an important vegetable crop belongs to family Cucurbitaceae. It contains astringent and antipyretic properties and used to treat constipation, indigestion, jaundice and dehydration. In a field survey 102 fruit and seeds samples were collected from various cucumber growing districts of Rajasthan to know the incidence of various diseases. The fruit samples exhibit discolouration and fungal growth were used to detect the primary and secondary phytochemical changes. Two naturally infected fruit samples (lab ac no Cu-F23 and Cu-F29) revealed heavy incidence of Fusarium oxysporum f.sp. cucumerinum were selected for study. The seeds were extracted from such infected fruits; dried in shade and used for further study. A comparative analysis of primary metabolites viz. total carbohydrates, proteins, lipids and phenols in seeds extracts from healthy and naturally infected fruits of cucumber was carried out. The dry weight of total soluble sugar (3.1, 4.8 mg/gm), total starch (1.3, 1.4 mg/gm), protein (17.33, 18.34 mg/gm), lipids (8.55, 9.55 mg/gm) and phenols (8.65, 8.99 mg/gm) analysis showed that highest concentration of proteins was recorded in healthy seeds whereas concentration of phenols was higher noted in naturally infected seeds.