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In this research we evaluated biodegradation, tissue response and general toxicity of nanofibrous poly(lactic acid) (PLA) and polycaprolactone (PCL) scaffolds produced by conventional method of electrospinning and using NanoMatrix3D<jats:sup>\u00ae<\/jats:sup> (NM3D<jats:sup>\u00ae<\/jats:sup>) technology.<\/jats:p><jats:p>Mass density, scanning electron microscopy and <jats:italic>in vitro<\/jats:italic> degradation (static and dynamic) were used for material characterization, and subcutaneous, intramuscular and intraperitoneal implantation \u2013 for <jats:italic>in vivo<\/jats:italic> tests. Biochemical blood analysis and histology were used to assess toxicity and tissue response. Pore size and fiber diameter did not differ in conventional and NM3D<jats:sup>\u00ae<\/jats:sup> PLA and PCL materials, but mass density was significantly lower in NM3D<jats:sup>\u00ae<\/jats:sup> ones. Scaffolds made by conventional method showed toxic effect during the <jats:italic>in\u2010vivo<\/jats:italic> tests due to residual concentration of chloroform that released with material degradation. NM3D<jats:sup>\u00ae<\/jats:sup> method allowed cleaning scaffolds from residual solutions that made them nontoxic and biocompatible. Subcutaneous, intramuscular and intraperitoneal implantation of PCL and PLA NM3D<jats:sup>\u00ae<\/jats:sup> electrospun nanofibrous scaffolds showed their appropriate cell conductive properties, tissue and vessels formation in all sites. Thus, NM3D<jats:sup>\u00ae<\/jats:sup> PCL and PLA nanofibrous electrospun scaffolds can be used in the field of tissue engineering, surgery, wound healing, drug delivery, and so forth, due to their unique properties, nontoxicity and biocompatibility. \u00a9 2018 Wiley Periodicals, Inc. 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