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Interstitial lung diseases (ILDs) are pathologies affecting the pulmonary interstitium and, less frequently, the alveolar and vascular epithelia. Bronchoalveolar lavage (BAL) is commonly used in ILD evaluation since it allows the sampling of the lower respiratory tract. The prognostic value of BAL cell counts in ILD is unknown. Flow cytometry quantification of lymphocytes and neutrophils in BAL of 1074 real-life consecutive patients were retrospectively correlated with clinical, radiological, anatomopathological, functional/spirometry, and evolutionary data. Cut-offs with predictive value were established at 7% and 5% for lymphocytes and neutrophils, respectively. Three risk stratification groups (Risk-LN) were established: FAVORABLE (lymphocytes > 7% and neutrophils < 5%), INTERMEDIATE (rest of patients), and UNFAVORABLE (lymphocytes < 7% and neutrophils > 5%), showing 75th percentile overall survival (OS) of 10.0 ± 1.4, 5.8 ± 0.6, and 3.0 ± 0.3 years (p < 0.001), respectively. A scoring model combining Risk-LN and the age of the patients with great predictive capacity for OS on fibrotic and non-fibrotic ILDs is proposed. This score is an independent predictive factor (HR = 1.859, p = 0.002) complementary to the fibrosis status (HR = 2.081, p < 0.001) and the type of treatment. Flow cytometry of BAL provides rapid and accurate quantification of lymphocytes and neutrophils, allowing the establishment of a risk score model that is useful in the clinical management of fibrotic and non-fibrotic ILDs from the time of diagnosis.