Germplasm of 153 flax (Linum usitatissimum) accessions from 24 countries held at Plant Gene Resources of Canada (PGRC) was evaluated for resistance to fusarium wilt (Fusarium oxysporum), anthracnose (Colletotrichum lini) and pasmo (Septoria linicola). The screening was conducted at the All-Russian Flax Research Institute (VNIIL) at Torzhok, Russia, over 3 years for fusarium wilt and anthracnose, and over 2 years for pasmo. A disease severity index ranging from 0% (no infection) to 100% (heavy infection) was calculated based on observations after artificial inoculation with the pathogens in the greenhouse (fusarium wilt) or in field nurseries (anthracnose and pasmo). The average disease severity index for fusarium wilt was 56.6 ± 34.4% (range 0–100.0%), for anthracnose 59.8 ± 8.1% (range 43.8–83.9%) and for pasmo 74.2 ± 11.8% (range 27.3–100.0%). The variation of disease severity indices among the years and within each accession was highest for fusarium wilt. Higher than average resistance for all three diseases was found in accessions from East Asia, while germplasm from the Indian subcontinent showed considerably lower than average resistance. Germplasm from North America and South America (mostly linseed) displayed above average resistance to fusarium wilt, while European accessions (mostly fibre flax) showed lower than average resistance to this disease. The different resistance levels reflected the improvements made by plant breeding and differences in the environments under which the germplasm accessions evolved. Accessions with potential use in linseed and fibre flax breeding were identified.