Plant-associated endophytic fungi are rich sources of novel bioactive and structurally diverse secondary metabolites and other natural products. Newly synthesized secondary metabolites of endophytes in terrestrial plants and their biological properties are presented and reviewed herein. The review highlights natural products from plant-associated fungal endophytes that demonstrate significant inhibition against pathogenic strains, human cancer cell lines and other biological targets. We have summarized 221 recently isolated, structurally diverse and novel secondary metabolites. Secondary metabolites that failed to demonstrate activity in the bioassays are not included. The review is intended to assist scientists in the fields of phytochemistry, organic chemistry, and pharmacology.