Breath analysis is rapidly evolving as a non-invasive disease recognition and diagnosis method. Metal oxide gas sensors are one of the most ideal platforms for realizing portable, hand-held breath analysis devices in the near future. This paper reviewed the recent developments in metal oxide gas sensors detecting exhaled biomarker gases such as nitric oxides, acetone, ammonia, hydrogen sulfide, and hydrocarbons. Emphasis was placed on strategies to tailor sensing materials/films capable of highly selective and sensitive detection of biomarker gases with negligible cross-response to ethanol, the major interfering breath gas. Specific examples were given to highlight the validity of the strategies, which include optimization of sensing temperature, doping additives, utilizing acid-base interaction, loading catalysts, and controlling gas reforming reaction. In addition, we briefly discussed the design and optimization method of gas sensor arrays for implementing the simultaneous assessment of multiple diseases. Breath analysis using high-performance metal oxide gas sensors/arrays will open new roads for point-of-care diagnosis of diseases such as asthma, diabetes, kidney dysfunction, halitosis, and lung cancer.