Podophyllotoxin (PTOX) is a natural antiviral, antirheumatic and anticancer molecule but its chemical synthesis is expensive. The present study aimed to develop and validate an analytical method by HPLC for the quantification of PTOX in roots of Hyptis suaveolens, as well as to evaluate the culture of its roots in vitro in liquid medium supplement with different concentrations of Indole-3-butyric acid (IBA), 1-Naphthaleneacetic acid (NAA), vitamins and myo-inositol. The analytical method was developed and validated. Root culture was used for biomass production and PTOX content was quantified using the developed analytical method after successful validation. The parameters that confirmed the analytical method were selectivity (peak purity: > 99%), system suitability (Rs = 2.92; N = 7064; k = 1.23; As = 1.31; DPR = 0.61%), intra-day and inter-day precision (DPR = 2.43% and 2.96%, respectively), linearity (R² = 0.997), recovery percentage (90.47–101.85%), limit of quantification (5.25 ng) and limit of detection (0.5 ng). Root culture in MS medium containing 1 mg L-1 IBA + 0.5 mg L-1 NAA showed the highest root dry weight (248.76 mg) and the highest PTOX concentration in the root (179, 97 µg-1). The vitamins and myo-inositol in the medium produced 198.88 mg of root dry weight and 6.01 µg g-1 of PTOX. The roots cultured in liquid MS medium supplemented with 1 mg L-1 of IBA + 0.5 mg L-1 of NAA maximized the root biomass and PTOX content. The adequate balance of vitamin and myo-inositol supplementation in liquid MS culture medium increased the production of root dry weight and PTOX accumulation.