Background: The cycle threshold (Ct) of real-time reverse transcription PCR (RT-qPCR) indicates the relative concentration of an RNA sequence, this value has been related to clinical profile in viral infections. Aim: To determine the correlation between the Ct value and the clinical classification of COVID-19. Method: A correlational cross-sectional study was carried out, the Ct values were obtained by RT-qPCR directed to the N gene of SARS-CoV-2, grouping them by means of a central robust estimator and related to the clinical classification of COVID-19. Results: Of the 718 cases included in the study; 77.7% (558) were mild; 21.3% (153) moderate and 1% (7) severe. The Ct value was grouped into levels: low Ct ≤ 18.83; medium Ct> 18.83-30.10 and high Ct> 30.10. There was a weak inverse significant correlation (p = 0.002; Spearman’s rho =-0.117) between the Ct value and the clinical classification. The characteristics: sex, age under 65 years, fever, chills, diarrhea, anosmia, and overweight-obesity were associated with the Ct value. Conclusion: The lower the Ct value, a classification of greater severity of COVID-19 is expected, however, because the correlation is weak, its usefulness as a severity predictor is limited. Keywords: coronavirus infections; polymerase chain reaction; viral load; cycle threshold.