One of the most important reasons for the high number of tuberculosis (TB)-related deaths in low-income countries is due to the challenge of diagnosis. The simple and cheaper light-emitting diode fluorescent microscopy (LED-FM) having long life-span, not producing ultraviolet (UV) light, minimal power requirements and better performance is recommended by the World Health Organization (WHO), in 2009 to replace the conventional microscopy in both high- and low-volume laboratories. The WHO has also endorsed (in 2010) one more technique, GeneXpert MTB/RIF assay (Xpert), for better TB diagnosis particularly among human immunodeficiency virus (HIV)-infected cases. However, the relative performance of both of these tools differs from setting to setting in reference to culture as a gold standard. This study was, thus, aimed at evaluating these tools for TB detection in individuals visiting Ambo Hospital, west-central Ethiopia. Cross-sectional early-morning sputum samples were collected from presumptive TB patients attending Ambo Hospital between January and August 2015. Socio-demographic data were captured using a semi-structured questionnaire. Clinical information was gathered from patientsâ€™ medical records. The sputum samples were diagnosed using LED-FM, Xpert, concentrated Ziehl-Neelsen (cZN) staining and Lowenstein-Jensen (LJ) medium culture. Drug sensitivity test (DST) was also conducted. Totally, 362 sputum samples were collected and processed. Of these, 36(9.9%) samples were positive by LED-FM, 42(11.6%) by cZN and 50(13.8%) by Xpert. All 362 samples were cultured but 22 were contaminated and 8 nontuberculous Mycobacteria (NTM) leaving only 332 with a definite culture status. From these 332, 45(13.6%) had culture-confirmed TB with 11(24.4%) being HIV co-infected. Two samples were rifampicin resistant by both DST and Xpert. The sensitivity, specificity, positive and negative predictive values of LED-FM and Xpert were 77.8, 100, 100 and 96; and 93.3, 98, 97.5 and 98.9% respectively. Xpert demonstrated 100 and 71.4% sensitivity in smear positive-culture positive and smear negative-culture positive sputum samples in detecting MTB respectively and increased MTB detection rate by 28% compared to dLED-FM.