The introduction of biological disease-modifying antirheumatic drug (bDMARD) treatments for various types of autoimmune arthritis, such as rheumatoid arthritis, psoriatic arthropathy and ankylosing spondylitis, represents a new era of treatment for patients with a refractory response to conventional synthetic DMARDs (csDMARDs). Many new bDMARDs with different modalities or that target different pro-inflammatory molecules, likely cytokines, are rapidly emerging. Hence, physicians in the field may be confused about choosing appropriate bDMARDs for their patients. Considering the high cost of bDMARDs and the rapid destructive process of autoimmune arthritis in patients, the choice of optimal bDMARDs for patients who fail to respond or show an inadequate therapeutic response to csDMARDs designed to control the disease is very critical. Here, we summarize the strengths and weaknesses of bDMARDs and specifically focus on their uses in patients with comorbid conditions or with specific medical conditions, such as pregnancy. This commentary provides a solid up-to-date review on commercially available bDMARDs and very useful information for physicians to facilitate the choice of more appropriate bDMARDs to treat patients with autoimmune arthritis and for basic researchers to understand the current strategies of bDMARD usage and hopefully to develop more powerful bDMARDs with fewer safety concerns.