Artificial intelligence (AI) and machine learning (ML) have advanced in several areas and fields of life; however, its progress in the field of multi-omics is not matching the levels others have attained. Challenges include but are not limited to the handling and analysis of high volumes of complex multi-omics data, and the expertise needed to implement and execute AI/ML approaches. In this article, we present IntelliGenes, an interactive, customizable, cross-platform, and user-friendly AI/ML application for multi-omics data exploration to discover novel biomarkers and predict rare, common, and complex diseases. The implemented methodology is based on a nexus of conventional statistical techniques and cutting-edge ML algorithms, which outperforms single algorithms and result in enhanced accuracy. The interactive and cross-platform graphical user interface of IntelliGenes is divided into three main sections: (i) Data Manager, (ii) AI/ML Analysis, and (iii) Visualization. Data Manager supports the user in loading and customizing the input data and list of existing biomarkers. AI/ML Analysis allows the user to apply default combinations of statistical and ML algorithms, as well as customize and create new AI/ML pipelines. Visualization provides options to interpret a diverse set of produced results, including performance metrics, disease predictions, and various charts. The performance of IntelliGenes has been successfully tested at variable in-house and peer-reviewed studies, and was able to correctly classify individuals as patients and predict disease with high accuracy. It stands apart primarily in its simplicity in use for nontechnical users and its emphasis on generating interpretable visualizations. We have designed and implemented IntelliGenes in a way that a user with or without computational background can apply AI/ML approaches to discover novel biomarkers and predict diseases.