Objectives Interstitial lung disease (ILD) is a common extra-muscular manifestation of anti-synthetase syndrome (ASS) and the main cause of morbidity and mortality in patients with ASS. Data on prognostic factors in these patients are lacking. Methods A total of 69 patients with ILD and positivity for at least one of the following autoantibodies were included: anti-Jo-1, anti-PL7, anti-PL12, and anti-EJ. Relevant clinical characteristics were registered. According to the changes in the extent of abnormalities at the follow-up on high-resolution computed tomography (HRCT), three groups were defined: the regression, stability, and deterioration groups. Univariate analysis was performed to evaluate possible prognostic factors and multivariate analysis by logistic regression was then applied to determine the independent prognostic factors in ASS-ILD. Results The cohort comprised 69 patients positive for anti-synthetase antibodies, i.e., 30 for anti-Jo-1, 16 for anti-EJ, 13 for anti-PL7, and 10 for anti-PL12. The mean length of follow-up was 15 months. Sex, age at diagnosis, fever at presentation, and counts of CD3(+)CD4(+) cells were significantly different among the three groups. According to the multivariate analysis, fever at presentation, lower counts of CD3(+)CD4(+) cells, and a pattern of usual interstitial pneumonia were the three independent risk factors for poor outcomes of ASS-ILD. Conclusions At the onset of ASS, some clinical features and HRCT pattern of ILD may suggest an unfavorable outcome of lung involvement on HRCT, even with routine therapy. These factors may contribute to the high long-term mortality of ASS.