Podophyllotoxin (PTOX) is a natural antiviral, antirheumatic and anticancer molecule, but it is expensive to chemically synthesize. The present study aimed to evaluate growth and PTOX accumulation in root cultures of Hyptis suaveolens treated with different concentrations of auxins, vitamins and myo-inositol. Root cultures grown in liquid medium supplemented with different concentrations of indole-3-butyric acid (IBA), 1-naphthaleneacetic acid (NAA), vitamins and myo-inositol were used to measure biomass production and PTOX content. PTOX quantitation was performed via high-performance liquid chromatography with diode-array detection (HPLC-DAD) using a newly developed analytical method after successful validation. Root culture in MS medium supplemented with 1 mg L−1 IBA +0.5 mg L−1 NAA resulted in the highest root dry weight (248.76 mg) and the highest PTOX concentration in the roots (179.97 μg g−1 root). The roots cultured in liquid MS medium supplemented with 1 mg L−1 IBA +0.5 mg L−1 NAA presented the greatest increase in root biomass and PTOX content. This adequate balance of vitamin and myo-inositol supplementation in liquid MS culture medium increased the root dry weight and PTOX content.