A BIST procedure is proposed for testing and fault tolerance of molecular electronics-based nanoFabrics. The nanoFabrics are assumed to include up to 1010 gates; this requires new test strategies that can efficiently test and diagnose the nanoFabric in a reasonable time. Our BIST procedure utilizes nanoFabric?s components as test pattern generator and response analyzer. The proposed technique tests the components in parallel with a low number of test configurations reducing the test time significantly. Due to high defect density of nanoFabrics, a diagnostic procedure needs to be done to achieve a high recovery. A defect database is created to be used by compilers during configuring the nanoFabric to avoid defective components. This results in a reliable system constructed using unreliable components.