This is the most difficult area to manage. Normally a sperm ejaculate contains at least 4% normally shaped sperm. This is unique in mammals. All other mammals have almost informally normal sperm.
Abnormal sperm are not usually genetically more abnormal. Therefore there is no extra risk of an abnormal baby. It does, however affect the swimming pattern of sperm. Sperm swim by oscillation (moving to and fro) and for instance an abnormal shaped sperm head might prevent straight line swimming and stop the sperm reaching the site of fertilisation in the fallopian tube. People with less than 2% normal sperm may have difficulty fertilising eggs and ICSI may be advised.
The number of abnormally formed sperm is known to be affected by the same toxins that may cause low count. Smoking is well known to increase the number of abnormally formed sperm in some men.
Testes work best at about 2 degrees below body temperature. Men with a varicocele often have higher numbers of abnormal sperm. Although treatment of the varicocele helps reduce this, currently the evidence is that varicocele treatment does not helps fertility.
An increase in abnormal sperm shape seems to affect natural conception rather than IVF/ICSI