Tat Activating Regulatory DNA Binding Protein (Tardbp or TDP-43), a highly conserved metazoan DNA/RNA binding protein thought to be involved in RNA transcription and splicing, has been linked to the pathophysiology of amyotrophic lateral sclerosis and frontotemporal lobar degeneration and is essential for early embryonic development. However, neither the physiological role of TDP-43 in the adult nor its downstream targets are well defined. To address these questions, we developed conditional Tardbp knockout mice and embryonic stem (ES) cell models. Here, we show that post-natal deletion of Tardbp in mice caused dramatic loss of body fat followed by rapid death. Moreover, conditional Tardbp knockout ES cells failed to proliferate. Importantly, high throughput DNA sequencing analysis on the transcriptome of ES cells lacking Tardbp revealed a set of downstream targets of TDP-43. We show that Tbc1d1, a gene known to mediate leanness and linked to obesity, is down-regulated in the absence of TDP-43. Collectively, our results establish that TDP-43 is critical for fat metabolism and ES cell survival. One allele of both iTDPKO and cTDP ES cells were replaced by CAG-ErCreEr. The other allele in iTDPKO ES cells is floxed exon3 while in the cTDP ES cells is wild type.