There is limited knowledge on prognostic factors for developing chronic low back pain (LBP) at an early stage of LBP. The objectives of this study were to investigate the clinical course of pain and disability, and prognostic factors for non-recovery after 1-year, in patients seeking help for the first time due to acute LBP. An inception cohort study included 123 patients with acute LBP lasting less than 3 weeks and consulting primary care for the first time. Main outcome measures were pain intensity, Roland–Morris disability questionnaire (RMQ), and sickness absence. Eleven patients (9%) did not return for the 12-month follow-up. There were large and significant reductions in pain intensity (P<0.001) and RMQ scores (P<0.001) during follow-up. Patients with neurological signs showed significantly less improvement in pain (P=0.001) and RMQ (P=0.004) compared with those without neurological signs. The proportions with sickness absence due to LBP at 6, 9, and 12 months were 7%, 8%, and 9%, respectively. At 12 months, 17% of patients had not fully recovered. Multivariate logistic regression analyses showed that high scores on a psychosocial screening (acute low back pain screening questionnaire) and emotional distress (Hopkin’s symptom check list) were significantly associated with non-recovery at 12 months, with odds ratios of 4.4 (95% confidence interval 1.1–17.4) and 3.3 (1.1–10.2), respectively.