Quinolone antibacterial agents are widely used in the clinic because of their high antibacterial activity, broad spectra and favorable pharmacokinetics. However, the adverse effects induced by quinolones, such as tendon/articular toxicity, central nervous system toxicity, phototoxicity and dysglycemia, have greatly restricted their therapeutic use. Differentiated embryo-chondrocyte expressed gene 1 (DEC1), an important transcription factor that has a basic helix-loop-helix domain and is ubiquitously expressed in both human embryonic and adult tissues, has a pivotal function in various biological phenomena, including neurogenesis, neuroregulation, chondrogenesis, cell growth, oncogenesis, immune balance and circandian rhythm. Recently, DEC1 has received increasing attention for its role in maintaining the homeostasis of metabolism and energy. Research has shown that DEC1 may play a vital role in metabolic disease. Although the mechanism of the adverse reactions caused by quinolones has not been clarified, the distribution of these serious adverse effects in tissues and organs is consistent with the expression of DEC1 in corresponding normal tissues. In the present paper, we review evidence showing that DEC1 may take part in the adverse effects induced by quinolone antibiotics. The investigation of the molecular details of the toxicity caused by quinolones may help overcome the shortcomings of the antibiotics and reveal new, useful therapeutic functions besides their antimicrobial effect.