Population-based data suggest that high intake of omega-3 (n-3) polyunsaturated fatty acids (PUFA) may be beneficial in a variety of health conditions. It is likely that mainly those patients with preexisting n-3 deficiency are those that benefit most from n-3 fatty acid supplementation. Therefore, for targeted interventions, a fast and reliable screening tool for n-3 PUFA intake is necessary. Thus, the aim of this project was to adapt and validate a food frequency questionnaire (FFQ) for n-3 PUFA intake in Switzerland while using as references the following: (1) 7-day food records (FR), and (2) n-3 fatty acid composition of red blood cells (RBC). We recruited 46 healthy adults for the first part of the study and 152 for the second. We used the dietary software EBISpro for the analysis of n-3 PUFA intake. RBC fatty acid composition was determined by gas chromatography mass spectrometry (GC-MS). Using correlation analysis, we found a moderate significant association between FFQ and FR for α-linolenic acid (ALA), eicosapentanoic acid (EPA), docosahexanoic acid (DHA), and total n-3 fatty acids (all r between 0.523 and 0.586, all p < 0.001). Bland Altman analysis further showed good agreement between the two methods and no proportional bias. Correlations between FFQ and RBC fatty acid composition were also moderate for EPA and DHA (r = 0.430 and r = 0.605, p < 0.001), but weaker for ALA and total n-3 (r = 0.314 and r = 0.211, p < 0.01). The efficacy of the FFQ to classify individuals into the same or adjacent quartile of RBC PUFA content ranged between 70% and 87% for the different fatty acids. In conclusion, we showed that the Swiss n-3 PUFA FFQ is a valid tool to assess dietary n-3 PUFA intake, especially DHA and EPA, to determine population groups at risk for low intake.