UK geneticists said that most flaws are "silent" mutations and do not affect health, although they can cause problems when passed to future generations.
Others are linked to conditions such as cancer or heart disease, which appear in later life, say geneticists.
The evidence comes from the 1,000 Genomes project, which is mapping normal human genetic differences, from tiny changes in Deoxyribonucleic acid (DNA) to major mutations, the BBC News reported.
In the study, 1,000 seemingly healthy people from Europe, the Americas and East Asia had their entire genetic sequences decoded, to look at what makes people different from each other, and to help in the search for genetic links to diseases.
The new research, published in The American Journal of Human Genetics, compared the genomes of 179 participants, who were healthy at the time their DNA was sampled, with a database of human mutations developed at Cardiff University.
It revealed that a normal healthy person has on average about 400 potentially damaging DNA variations, and two DNA changes known to be associated with disease.
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"Ordinary people carry disease-causing mutations without them having any obvious effect," said Dr Chris Tyler-Smith, lead researcher on the study from the Wellcome Trust Sanger Institute, Cambridge.
"In a population there will be variants that have consequences for their own health," Tyler-Smith said.
"The research gives an insight into the flaws that make us all different, sometimes with different expertise and different abilities, but also different predispositions in diseases," said Professor David Cooper of Cardiff University, the other lead researcher of the study.
"Not all human genomes have perfect sequences. The human genome is packed with pervasive, architectural flaws," he said.
It has been known for decades that all people carry some genetic mutations that appear to cause little or no harm. Many are only damaging if they are passed on to children who inherit another copy of the faulty gene from the other parent.
In others - around one in ten of those studied - the mutation causes only a mild condition, appears to be inactive, or does not manifest itself until later life.
"All of our genomes contain flaws; some of us will carry deleterious variants but will not be at risk of acquiring the associated disease for one reason or another," Tyler-Smith said.
"For others, there will be health consequences, and early warning could be useful, but might still come as an unwelcome surprise to the participant," he added.