Tuberculosis (TB) is a disease in Indonesia with the second largest number of cases in the world after India. One of the TB-free strategies is early diagnosis with bacteriological laboratory examination for rapid treatment, thereby reducing the incidence rate. WHO recommends the GeneXpert molecular rapid test for confirming the diagnosis of TB. The TB diagnosis is confirmed by Acid-Fast Bacilli (AFB) microscopic examination for laboratories with difficulty accessing rapid molecular tests. The study aims to compare the rapid molecular test GeneXpert MTB/RIF Ultra examination with Ziehl-Neelsen stained AFB microscopic examination in diagnosing lung patients who have been detected with Mycobacterium tuberculosis very low, low, medium, and High (MTB detected)—the type of observational analytical study, with a cross-sectional design to understand the differences. The sampling technique is a total sampling of 30 samples, and data analysis using the Wilcoxon statistical test. Of the 30 samples tested for Mycobacterium tuberculosis (MTB), the Molecular Rapid Test identified all samples as positive (100%). In contrast, AFB microscopy detected only 23 positive cases (76.67%) and failed to detect MTB in 7 samples (23.33%). Based on bacterial load classification, three samples (10%) were categorized as very low, with AFB results showing two negatives (6.67%) and one scanty (3.33%). Among the nine low-load samples (30%), five were AFB-negative (16.67%) and four were positive (1+) (13.33%). In the seven medium-load samples (23.33%), microscopy detected five samples as 1+ (16.67%), two as 2+ (6.67%), and one as 3+ (3.33%). Of the 11 high-load samples (36.67%), AFB identified three as 2+ (10%) and eight as 3+ (23.33%). The conclusion of the results of the Molecular Rapid Test examination with AFB microscopic there shows a significant difference (P < 0.025) < ? (0.05). It is recommended that further research be conducted to compare three bacteriological examinations, namely rapid molecular test, AFB microscopic, and culture, as a gold standard examination.